File formats

AlphaPeel works with multiple files, which have specific formats. Sometimes there are specific details related either to input or output of these files. The following describes the format and any input and output specific details for each file.

Table of Contents

• Allele and genotype encoding
• Data file formats
  • Pedigree
  • Genotype
  • Dosage
  • Sequence allele read counts
  • Haplotype
  • Phenotype
  • Genotype probability
  • Phased genotype probability
  • Map
  • Segregation probability
  • Phenotype probability
• Parameter file formats
  • Alternative allele probability
  • Genotype error probability
  • Sequence error probability
  • Phenotype penetrance probability